Description
Follow-up analyses of GWIS findings
- Table of significant and suggestive (1df GxE only)
vegetable5qcm GWIS findings
- GxE models stratified by study_design and tumor site (proximal, distal, rectal)
- GxE models with additional covariate sets (might do this for aspirin ..)
- Odds ratios stratified by exposure and genotype
- Plots of model predicted outcome by 1 unit increase of exposure/allelic dosage
- Locuszoom plot
- Functional annotation plot
3DF
Output models stratified by sex or tumor site to check for differences in associations
chr4_91049759_C_G
Allele Freq

GxE stratified by sex
sex stratified chr4_91049759_C_G_dose x vegetable5qcm_scaled
|
|
|
|
Dependent variable:
|
|
|
|
|
|
outcome
|
|
|
All (Ca=29896,Co=39838)
|
Female (Ca=14493,Co=19608)
|
Male (Ca=15403,Co=20230)
|
|
|
(1)
|
(2)
|
(3)
|
|
|
|
chr4_91049759_C_G_dose
|
0.947 (0.800, 1.094)
|
0.853 (0.638, 1.068)
|
1.036 (0.834, 1.238)
|
|
vegetable5qcm_scaled
|
0.873*** (0.841, 0.904)
|
0.874*** (0.829, 0.920)
|
0.868*** (0.824, 0.913)
|
|
age_ref_imp
|
1.000 (0.998, 1.002)
|
1.000 (0.998, 1.003)
|
1.000 (0.997, 1.002)
|
|
energytot_imp
|
1.000*** (1.000, 1.000)
|
1.000*** (1.000, 1.000)
|
1.000*** (1.000, 1.000)
|
|
sex
|
0.979 (0.943, 1.015)
|
|
|
|
chr4_91049759_C_G_dose:vegetable5qcm_scaled
|
1.055 (0.943, 1.167)
|
1.101 (0.930, 1.272)
|
1.018 (0.869, 1.167)
|
|
Constant
|
0.975 (0.814, 1.135)
|
0.887 (0.652, 1.122)
|
1.025 (0.803, 1.247)
|
|
|
|
Observations
|
69,734
|
34,101
|
35,633
|
|
|
|
Note:
|
p<0.05; p<0.01; p<0.001
|
|
|
(PC and Study estimates omitted from table)
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|
|
GxE term LRtest p = 3.5059e-01
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|
|
GxE term LRtest p = 2.7064e-01
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|
|
GxE term LRtest p = 8.1489e-01
|
GxE stratified by tumor site
cancer_site_sum2 stratified chr4_91049759_C_G_dose x vegetable5qcm_scaled
|
|
|
|
Dependent variable:
|
|
|
|
|
|
outcome
|
|
|
All (Ca=29896,Co=39838)
|
Proximal (Ca=9067,Co=39838)
|
Distal (Ca=10542,Co=39838)
|
Rectal (Ca=8432,Co=39838)
|
|
|
(1)
|
(2)
|
(3)
|
(4)
|
|
|
|
chr4_91049759_C_G_dose
|
0.947 (0.800, 1.094)
|
0.871 (0.646, 1.096)
|
0.929 (0.721, 1.138)
|
1.119 (0.909, 1.330)
|
|
vegetable5qcm_scaled
|
0.873*** (0.841, 0.904)
|
0.874*** (0.829, 0.920)
|
0.884*** (0.840, 0.928)
|
0.860*** (0.810, 0.909)
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|
age_ref_imp
|
1.000 (0.998, 1.002)
|
0.995*** (0.992, 0.997)
|
1.018*** (1.016, 1.021)
|
0.985*** (0.983, 0.988)
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|
energytot_imp
|
1.000*** (1.000, 1.000)
|
1.000*** (1.000, 1.000)
|
1.000*** (1.000, 1.000)
|
1.000*** (1.000, 1.000)
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sex
|
0.979 (0.943, 1.015)
|
1.018 (0.966, 1.071)
|
0.785*** (0.733, 0.836)
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1.239*** (1.183, 1.294)
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chr4_91049759_C_G_dose:vegetable5qcm_scaled
|
1.055 (0.943, 1.167)
|
1.046 (0.876, 1.215)
|
1.062 (0.903, 1.221)
|
0.948 (0.783, 1.114)
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|
Constant
|
0.975 (0.814, 1.135)
|
0.576*** (0.353, 0.799)
|
0.100*** (-0.136, 0.337)
|
0.581*** (0.344, 0.818)
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|
|
|
Observations
|
69,734
|
48,905
|
50,380
|
48,270
|
|
|
|
Note:
|
p<0.05; p<0.01; p<0.001
|
|
|
(PC and Study estimates omitted from table)
|
|
|
GxE term LRtest p = 3.5059e-01
|
|
|
GxE term LRtest p = 6.0457e-01
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GxE term LRtest p = 4.5820e-01
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|
|
GxE term LRtest p = 5.2879e-01
|
GxE stratified by study design
study_design stratified chr4_91049759_C_G_dose x vegetable5qcm_scaled
|
|
|
|
Dependent variable:
|
|
|
|
|
|
outcome
|
|
|
All (Ca=29896,Co=39838)
|
Cohort (Ca=12549,Co=24275)
|
Case-Control (Ca=17347,Co=15563)
|
|
|
(1)
|
(2)
|
(3)
|
|
|
|
chr4_91049759_C_G_dose
|
0.947 (0.800, 1.094)
|
0.846 (0.611, 1.082)
|
1.018 (0.826, 1.210)
|
|
vegetable5qcm_scaled
|
0.873*** (0.841, 0.904)
|
0.936* (0.885, 0.988)
|
0.836*** (0.796, 0.875)
|
|
age_ref_imp
|
1.000 (0.998, 1.002)
|
1.002 (0.999, 1.005)
|
0.999 (0.997, 1.001)
|
|
energytot_imp
|
1.000*** (1.000, 1.000)
|
1.000 (1.000, 1.000)
|
1.000*** (1.000, 1.000)
|
|
sex
|
0.979 (0.943, 1.015)
|
0.993 (0.936, 1.050)
|
0.966 (0.920, 1.012)
|
|
chr4_91049759_C_G_dose:vegetable5qcm_scaled
|
1.055 (0.943, 1.167)
|
1.269 (0.922, 1.615)
|
1.008 (0.876, 1.140)
|
|
Constant
|
0.975 (0.814, 1.135)
|
3.634*** (3.180, 4.087)
|
1.097 (0.909, 1.285)
|
|
|
|
Observations
|
69,734
|
36,824
|
32,910
|
|
|
|
Note:
|
p<0.05; p<0.01; p<0.001
|
|
|
(PC and Study estimates omitted from table)
|
|
|
GxE term LRtest p = 3.5059e-01
|
|
|
GxE term LRtest p = 1.7696e-01
|
|
|
GxE term LRtest p = 9.0934e-01
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Odds Ratios
Variable is scaled by the median sex/study specific IQR, THEN centered around median / IQR (e.g. ref = median, comparison group = median + 1IQR)
|
|
G param by E
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|
|
CC
|
CG
|
GG
|
CG
|
GG
|
|
vegetable5qcm_scaled=0
|
1
|
0.93 (0.8-1.08)
|
1.49 (0.49-4.54)
|
0.93 (0.8-1.08)
|
1.49 (0.49-4.54)
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p0
|
P= 1
|
P= 0.34
|
P= 0.48
|
P= 0.34
|
P= 0.84
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|
vegetable5qcm_scaled=1
|
0.87 (0.85-0.9)
|
0.86 (0.76-0.97)
|
1.08 (0.54-2.19)
|
0.99 (0.88-1.11)
|
1.24 (0.62-2.5)
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p1
|
P= 1.7e-17
|
P= 0.017
|
P= 0.82
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P= 0.48
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P= 0.54
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E param by G
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|
vegetable5qcm_scaled
|
0.87 (0.85-0.9)
|
0.93 (0.83-1.04)
|
0.73 (0.31-1.7)
|
|
|
|
p
|
P= 1.7e-17
|
P= 0.22
|
P= 0.46
|
|
|
Interaction Plot
Variable is scaled by the median sex/study specific IQR, THEN centered around median / IQR (e.g. ref = median, comparison group = median + 1IQR) 
Locuszoom

Func Annot

Case-only
Output models stratified by sex or tumor site to check for differences in associations
chr16_70722103_G_C
Allele Freq

GxE stratified by sex
sex stratified chr16_70722103_G_C_dose x vegetable5qcm_scaled
|
|
|
|
Dependent variable:
|
|
|
|
|
|
outcome
|
|
|
All (Ca=29896,Co=39838)
|
Female (Ca=14493,Co=19608)
|
Male (Ca=15403,Co=20230)
|
|
|
(1)
|
(2)
|
(3)
|
|
|
|
chr16_70722103_G_C_dose
|
0.914 (0.822, 1.007)
|
0.879 (0.744, 1.014)
|
0.950 (0.822, 1.078)
|
|
vegetable5qcm_scaled
|
0.868*** (0.837, 0.900)
|
0.871*** (0.826, 0.917)
|
0.862*** (0.817, 0.907)
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|
age_ref_imp
|
1.000 (0.998, 1.002)
|
1.000 (0.998, 1.003)
|
1.000 (0.997, 1.002)
|
|
energytot_imp
|
1.000*** (1.000, 1.000)
|
1.000*** (1.000, 1.000)
|
1.000*** (1.000, 1.000)
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|
sex
|
0.978 (0.942, 1.014)
|
|
|
|
chr16_70722103_G_C_dose:vegetable5qcm_scaled
|
1.112** (1.035, 1.189)
|
1.120 (1.002, 1.239)
|
1.102 (1.000, 1.204)
|
|
Constant
|
0.977 (0.816, 1.137)
|
0.889 (0.654, 1.124)
|
1.027 (0.805, 1.249)
|
|
|
|
Observations
|
69,734
|
34,101
|
35,633
|
|
|
|
Note:
|
p<0.05; p<0.01; p<0.001
|
|
|
(PC and Study estimates omitted from table)
|
|
|
GxE term LRtest p = 6.9667e-03
|
|
|
GxE term LRtest p = 5.9571e-02
|
|
|
GxE term LRtest p = 6.2158e-02
|
GxE stratified by tumor site
cancer_site_sum2 stratified chr16_70722103_G_C_dose x vegetable5qcm_scaled
|
|
|
|
Dependent variable:
|
|
|
|
|
|
outcome
|
|
|
All (Ca=29896,Co=39838)
|
Proximal (Ca=9067,Co=39838)
|
Distal (Ca=10542,Co=39838)
|
Rectal (Ca=8432,Co=39838)
|
|
|
(1)
|
(2)
|
(3)
|
(4)
|
|
|
|
chr16_70722103_G_C_dose
|
0.914 (0.822, 1.007)
|
0.766*** (0.616, 0.916)
|
0.937 (0.803, 1.071)
|
1.023 (0.883, 1.164)
|
|
vegetable5qcm_scaled
|
0.868*** (0.837, 0.900)
|
0.868*** (0.822, 0.913)
|
0.878*** (0.834, 0.922)
|
0.853*** (0.803, 0.903)
|
|
age_ref_imp
|
1.000 (0.998, 1.002)
|
0.995*** (0.993, 0.998)
|
1.018*** (1.016, 1.021)
|
0.985*** (0.983, 0.988)
|
|
energytot_imp
|
1.000*** (1.000, 1.000)
|
1.000*** (1.000, 1.000)
|
1.000*** (1.000, 1.000)
|
1.000*** (1.000, 1.000)
|
|
sex
|
0.978 (0.942, 1.014)
|
1.017 (0.965, 1.070)
|
0.784*** (0.733, 0.836)
|
1.237*** (1.182, 1.293)
|
|
chr16_70722103_G_C_dose:vegetable5qcm_scaled
|
1.112** (1.035, 1.189)
|
1.168* (1.049, 1.286)
|
1.143* (1.033, 1.252)
|
1.078 (0.963, 1.193)
|
|
Constant
|
0.977 (0.816, 1.137)
|
0.577*** (0.354, 0.800)
|
0.101*** (-0.136, 0.337)
|
0.582*** (0.345, 0.819)
|
|
|
|
Observations
|
69,734
|
48,905
|
50,380
|
48,270
|
|
|
|
Note:
|
p<0.05; p<0.01; p<0.001
|
|
|
(PC and Study estimates omitted from table)
|
|
|
GxE term LRtest p = 6.9667e-03
|
|
|
GxE term LRtest p = 1.0792e-02
|
|
|
GxE term LRtest p = 1.7406e-02
|
|
|
GxE term LRtest p = 2.0394e-01
|
GxE stratified by study design
study_design stratified chr16_70722103_G_C_dose x vegetable5qcm_scaled
|
|
|
|
Dependent variable:
|
|
|
|
|
|
outcome
|
|
|
All (Ca=29896,Co=39838)
|
Cohort (Ca=12549,Co=24275)
|
Case-Control (Ca=17347,Co=15563)
|
|
|
(1)
|
(2)
|
(3)
|
|
|
|
chr16_70722103_G_C_dose
|
0.914 (0.822, 1.007)
|
0.944 (0.814, 1.073)
|
0.876 (0.742, 1.011)
|
|
vegetable5qcm_scaled
|
0.868*** (0.837, 0.900)
|
0.936* (0.884, 0.987)
|
0.827*** (0.787, 0.867)
|
|
age_ref_imp
|
1.000 (0.998, 1.002)
|
1.002 (0.999, 1.006)
|
0.999 (0.997, 1.001)
|
|
energytot_imp
|
1.000*** (1.000, 1.000)
|
1.000 (1.000, 1.000)
|
1.000*** (1.000, 1.000)
|
|
sex
|
0.978 (0.942, 1.014)
|
0.993 (0.936, 1.049)
|
0.965 (0.919, 1.011)
|
|
chr16_70722103_G_C_dose:vegetable5qcm_scaled
|
1.112** (1.035, 1.189)
|
1.102 (0.928, 1.277)
|
1.138** (1.042, 1.233)
|
|
Constant
|
0.977 (0.816, 1.137)
|
3.635*** (3.181, 4.088)
|
1.102 (0.914, 1.290)
|
|
|
|
Observations
|
69,734
|
36,824
|
32,910
|
|
|
|
Note:
|
p<0.05; p<0.01; p<0.001
|
|
|
(PC and Study estimates omitted from table)
|
|
|
GxE term LRtest p = 6.9667e-03
|
|
|
GxE term LRtest p = 2.7212e-01
|
|
|
GxE term LRtest p = 7.8922e-03
|
Odds Ratios
Variable is scaled by the median sex/study specific IQR, THEN centered around median / IQR (e.g. ref = median, comparison group = median + 1IQR)
|
|
G param by E
|
|
|
GG
|
GC
|
CC
|
GC
|
CC
|
|
vegetable5qcm_scaled=0
|
1
|
0.92 (0.83-1.01)
|
0.78 (0.32-1.91)
|
0.92 (0.83-1.01)
|
0.78 (0.32-1.91)
|
|
p0
|
P= 1
|
P= 0.072
|
P= 0.59
|
P= 0.072
|
P= 0.55
|
|
vegetable5qcm_scaled=1
|
0.87 (0.84-0.9)
|
0.89 (0.81-0.98)
|
0.73 (0.39-1.38)
|
1.03 (0.94-1.12)
|
0.84 (0.44-1.59)
|
|
p1
|
P= 1.3e-18
|
P= 0.013
|
P= 0.33
|
P= 0.59
|
P= 0.59
|
|
E param by G
|
|
vegetable5qcm_scaled
|
0.87 (0.84-0.9)
|
0.97 (0.9-1.06)
|
0.93 (0.52-1.69)
|
|
|
|
p
|
P= 1.3e-18
|
P= 0.51
|
P= 0.82
|
|
|
Interaction Plot
Variable is scaled by the median sex/study specific IQR, THEN centered around median / IQR (e.g. ref = median, comparison group = median + 1IQR) 
Locuszoom

Func Annot

Two-step (excluding GWAS loci)
chr5_112341879_T_C
Allele Freq

GxE stratified by sex
sex stratified chr5_112341879_T_C_dose x vegetable5qcm_scaled
|
|
|
|
Dependent variable:
|
|
|
|
|
|
outcome
|
|
|
All (Ca=29896,Co=39838)
|
Female (Ca=14493,Co=19608)
|
Male (Ca=15403,Co=20230)
|
|
|
(1)
|
(2)
|
(3)
|
|
|
|
chr5_112341879_T_C_dose
|
1.177** (1.076, 1.279)
|
1.025 (0.877, 1.173)
|
1.328*** (1.189, 1.467)
|
|
vegetable5qcm_scaled
|
0.869*** (0.837, 0.900)
|
0.869*** (0.823, 0.914)
|
0.864*** (0.820, 0.909)
|
|
age_ref_imp
|
1.000 (0.998, 1.002)
|
1.000 (0.998, 1.003)
|
1.000 (0.997, 1.002)
|
|
energytot_imp
|
1.000*** (1.000, 1.000)
|
1.000*** (1.000, 1.000)
|
1.000*** (1.000, 1.000)
|
|
sex
|
0.979 (0.943, 1.015)
|
|
|
|
chr5_112341879_T_C_dose:vegetable5qcm_scaled
|
1.145** (1.054, 1.235)
|
1.228** (1.094, 1.361)
|
1.088 (0.965, 1.211)
|
|
Constant
|
0.969 (0.808, 1.130)
|
0.883 (0.648, 1.118)
|
1.019 (0.797, 1.242)
|
|
|
|
Observations
|
69,734
|
34,101
|
35,633
|
|
|
|
Note:
|
p<0.05; p<0.01; p<0.001
|
|
|
(PC and Study estimates omitted from table)
|
|
|
GxE term LRtest p = 3.0645e-03
|
|
|
GxE term LRtest p = 2.2313e-03
|
|
|
GxE term LRtest p = 1.7725e-01
|
GxE stratified by tumor site
cancer_site_sum2 stratified chr5_112341879_T_C_dose x vegetable5qcm_scaled
|
|
|
|
Dependent variable:
|
|
|
|
|
|
outcome
|
|
|
All (Ca=29896,Co=39838)
|
Proximal (Ca=9067,Co=39838)
|
Distal (Ca=10542,Co=39838)
|
Rectal (Ca=8432,Co=39838)
|
|
|
(1)
|
(2)
|
(3)
|
(4)
|
|
|
|
chr5_112341879_T_C_dose
|
1.177** (1.076, 1.279)
|
1.161 (1.011, 1.310)
|
1.130 (0.985, 1.274)
|
1.231** (1.080, 1.383)
|
|
vegetable5qcm_scaled
|
0.869*** (0.837, 0.900)
|
0.865*** (0.819, 0.911)
|
0.884*** (0.841, 0.928)
|
0.849*** (0.799, 0.899)
|
|
age_ref_imp
|
1.000 (0.998, 1.002)
|
0.995*** (0.993, 0.998)
|
1.018*** (1.016, 1.021)
|
0.985*** (0.983, 0.988)
|
|
energytot_imp
|
1.000*** (1.000, 1.000)
|
1.000*** (1.000, 1.000)
|
1.000*** (1.000, 1.000)
|
1.000*** (1.000, 1.000)
|
|
sex
|
0.979 (0.943, 1.015)
|
1.019 (0.966, 1.072)
|
0.785*** (0.734, 0.837)
|
1.240*** (1.184, 1.295)
|
|
chr5_112341879_T_C_dose:vegetable5qcm_scaled
|
1.145** (1.054, 1.235)
|
1.249*** (1.123, 1.374)
|
1.042 (0.909, 1.176)
|
1.191** (1.062, 1.320)
|
|
Constant
|
0.969 (0.808, 1.130)
|
0.570*** (0.347, 0.793)
|
0.100*** (-0.137, 0.336)
|
0.578*** (0.341, 0.815)
|
|
|
|
Observations
|
69,734
|
48,905
|
50,380
|
48,270
|
|
|
|
Note:
|
p<0.05; p<0.01; p<0.001
|
|
|
(PC and Study estimates omitted from table)
|
|
|
GxE term LRtest p = 3.0645e-03
|
|
|
GxE term LRtest p = 5.2089e-04
|
|
|
GxE term LRtest p = 5.4377e-01
|
|
|
GxE term LRtest p = 8.2200e-03
|
GxE stratified by study design
study_design stratified chr5_112341879_T_C_dose x vegetable5qcm_scaled
|
|
|
|
Dependent variable:
|
|
|
|
|
|
outcome
|
|
|
All (Ca=29896,Co=39838)
|
Cohort (Ca=12549,Co=24275)
|
Case-Control (Ca=17347,Co=15563)
|
|
|
(1)
|
(2)
|
(3)
|
|
|
|
chr5_112341879_T_C_dose
|
1.177** (1.076, 1.279)
|
1.166* (1.024, 1.308)
|
1.166* (1.020, 1.311)
|
|
vegetable5qcm_scaled
|
0.869*** (0.837, 0.900)
|
0.938* (0.886, 0.989)
|
0.828*** (0.788, 0.868)
|
|
age_ref_imp
|
1.000 (0.998, 1.002)
|
1.002 (0.999, 1.006)
|
0.999 (0.997, 1.001)
|
|
energytot_imp
|
1.000*** (1.000, 1.000)
|
1.000 (1.000, 1.000)
|
1.000*** (1.000, 1.000)
|
|
sex
|
0.979 (0.943, 1.015)
|
0.993 (0.936, 1.050)
|
0.966 (0.920, 1.012)
|
|
chr5_112341879_T_C_dose:vegetable5qcm_scaled
|
1.145** (1.054, 1.235)
|
1.041 (0.841, 1.242)
|
1.173** (1.062, 1.283)
|
|
Constant
|
0.969 (0.808, 1.130)
|
3.603*** (3.149, 4.056)
|
1.093 (0.905, 1.282)
|
|
|
|
Observations
|
69,734
|
36,824
|
32,910
|
|
|
|
Note:
|
p<0.05; p<0.01; p<0.001
|
|
|
(PC and Study estimates omitted from table)
|
|
|
GxE term LRtest p = 3.0645e-03
|
|
|
GxE term LRtest p = 6.9294e-01
|
|
|
GxE term LRtest p = 4.4907e-03
|
Odds Ratios
Variable is scaled by the median sex/study specific IQR, THEN centered around median / IQR (e.g. ref = median, comparison group = median + 1IQR)
|
|
G param by E
|
|
|
TT
|
TC
|
CC
|
TC
|
CC
|
|
vegetable5qcm_scaled=0
|
1
|
1.19 (1.08-1.33)
|
0.86 (0.36-2.06)
|
1.19 (1.08-1.33)
|
0.86 (0.36-2.06)
|
|
p0
|
P= 1
|
P= 0.00085
|
P= 0.73
|
P= 0.00085
|
P= 4.1e-09
|
|
vegetable5qcm_scaled=1
|
0.87 (0.84-0.9)
|
1.17 (1.06-1.3)
|
1.4 (0.67-2.92)
|
1.35 (1.22-1.5)
|
1.61 (0.78-3.36)
|
|
p1
|
P= 1.6e-18
|
P= 0.0023
|
P= 0.37
|
P= 0.73
|
P= 0.2
|
|
E param by G
|
|
vegetable5qcm_scaled
|
0.87 (0.84-0.9)
|
0.98 (0.9-1.08)
|
1.63 (0.76-3.52)
|
|
|
|
p
|
P= 1.6e-18
|
P= 0.74
|
P= 0.21
|
|
|
Interaction Plot
Variable is scaled by the median sex/study specific IQR, THEN centered around median / IQR (e.g. ref = median, comparison group = median + 1IQR) 
Locuszoom

Func Annot

chr5_112500404_T_C
Allele Freq

GxE stratified by sex
sex stratified chr5_112500404_T_C_dose x vegetable5qcm_scaled
|
|
|
|
Dependent variable:
|
|
|
|
|
|
outcome
|
|
|
All (Ca=29896,Co=39838)
|
Female (Ca=14493,Co=19608)
|
Male (Ca=15403,Co=20230)
|
|
|
(1)
|
(2)
|
(3)
|
|
|
|
chr5_112500404_T_C_dose
|
1.166* (1.030, 1.302)
|
1.131 (0.935, 1.327)
|
1.188 (0.999, 1.377)
|
|
vegetable5qcm_scaled
|
0.869*** (0.838, 0.900)
|
0.870*** (0.825, 0.916)
|
0.865*** (0.821, 0.909)
|
|
age_ref_imp
|
1.000 (0.998, 1.002)
|
1.001 (0.998, 1.003)
|
1.000 (0.997, 1.002)
|
|
energytot_imp
|
1.000*** (1.000, 1.000)
|
1.000*** (1.000, 1.000)
|
1.000*** (1.000, 1.000)
|
|
sex
|
0.979 (0.943, 1.015)
|
|
|
|
chr5_112500404_T_C_dose:vegetable5qcm_scaled
|
1.199** (1.090, 1.307)
|
1.301** (1.137, 1.466)
|
1.123 (0.978, 1.269)
|
|
Constant
|
0.974 (0.813, 1.135)
|
0.882 (0.647, 1.117)
|
1.030 (0.807, 1.252)
|
|
|
|
Observations
|
69,734
|
34,101
|
35,633
|
|
|
|
Note:
|
p<0.05; p<0.01; p<0.001
|
|
|
(PC and Study estimates omitted from table)
|
|
|
GxE term LRtest p = 9.6238e-04
|
|
|
GxE term LRtest p = 1.3470e-03
|
|
|
GxE term LRtest p = 1.1535e-01
|
GxE stratified by tumor site
cancer_site_sum2 stratified chr5_112500404_T_C_dose x vegetable5qcm_scaled
|
|
|
|
Dependent variable:
|
|
|
|
|
|
outcome
|
|
|
All (Ca=29896,Co=39838)
|
Proximal (Ca=9067,Co=39838)
|
Distal (Ca=10542,Co=39838)
|
Rectal (Ca=8432,Co=39838)
|
|
|
(1)
|
(2)
|
(3)
|
(4)
|
|
|
|
chr5_112500404_T_C_dose
|
1.166* (1.030, 1.302)
|
1.229* (1.034, 1.425)
|
1.047 (0.848, 1.247)
|
1.314** (1.116, 1.512)
|
|
vegetable5qcm_scaled
|
0.869*** (0.838, 0.900)
|
0.870*** (0.824, 0.915)
|
0.882*** (0.838, 0.926)
|
0.852*** (0.802, 0.901)
|
|
age_ref_imp
|
1.000 (0.998, 1.002)
|
0.995*** (0.993, 0.998)
|
1.018*** (1.016, 1.021)
|
0.985*** (0.983, 0.988)
|
|
energytot_imp
|
1.000*** (1.000, 1.000)
|
1.000*** (1.000, 1.000)
|
1.000*** (1.000, 1.000)
|
1.000*** (1.000, 1.000)
|
|
sex
|
0.979 (0.943, 1.015)
|
1.018 (0.965, 1.071)
|
0.785*** (0.733, 0.836)
|
1.239*** (1.184, 1.294)
|
|
chr5_112500404_T_C_dose:vegetable5qcm_scaled
|
1.199** (1.090, 1.307)
|
1.220** (1.070, 1.370)
|
1.153 (0.995, 1.312)
|
1.199* (1.048, 1.349)
|
|
Constant
|
0.974 (0.813, 1.135)
|
0.572*** (0.349, 0.795)
|
0.100*** (-0.136, 0.337)
|
0.581*** (0.344, 0.818)
|
|
|
|
Observations
|
69,734
|
48,905
|
50,380
|
48,270
|
|
|
|
Note:
|
p<0.05; p<0.01; p<0.001
|
|
|
(PC and Study estimates omitted from table)
|
|
|
GxE term LRtest p = 9.6238e-04
|
|
|
GxE term LRtest p = 9.3777e-03
|
|
|
GxE term LRtest p = 7.9311e-02
|
|
|
GxE term LRtest p = 1.8479e-02
|
GxE stratified by study design
study_design stratified chr5_112500404_T_C_dose x vegetable5qcm_scaled
|
|
|
|
Dependent variable:
|
|
|
|
|
|
outcome
|
|
|
All (Ca=29896,Co=39838)
|
Cohort (Ca=12549,Co=24275)
|
Case-Control (Ca=17347,Co=15563)
|
|
|
(1)
|
(2)
|
(3)
|
|
|
|
chr5_112500404_T_C_dose
|
1.166* (1.030, 1.302)
|
1.209 (1.012, 1.406)
|
1.153 (0.959, 1.347)
|
|
vegetable5qcm_scaled
|
0.869*** (0.838, 0.900)
|
0.934** (0.882, 0.985)
|
0.830*** (0.790, 0.869)
|
|
age_ref_imp
|
1.000 (0.998, 1.002)
|
1.002 (0.999, 1.006)
|
0.999 (0.997, 1.001)
|
|
energytot_imp
|
1.000*** (1.000, 1.000)
|
1.000 (1.000, 1.000)
|
1.000*** (1.000, 1.000)
|
|
sex
|
0.979 (0.943, 1.015)
|
0.994 (0.937, 1.050)
|
0.966 (0.919, 1.012)
|
|
chr5_112500404_T_C_dose:vegetable5qcm_scaled
|
1.199** (1.090, 1.307)
|
1.506** (1.219, 1.794)
|
1.177* (1.044, 1.310)
|
|
Constant
|
0.974 (0.813, 1.135)
|
3.589*** (3.136, 4.043)
|
1.099 (0.910, 1.287)
|
|
|
|
Observations
|
69,734
|
36,824
|
32,910
|
|
|
|
Note:
|
p<0.05; p<0.01; p<0.001
|
|
|
(PC and Study estimates omitted from table)
|
|
|
GxE term LRtest p = 9.6238e-04
|
|
|
GxE term LRtest p = 4.3001e-03
|
|
|
GxE term LRtest p = 1.6174e-02
|
Odds Ratios
Variable is scaled by the median sex/study specific IQR, THEN centered around median / IQR (e.g. ref = median, comparison group = median + 1IQR)
|
|
G param by E
|
|
|
TT
|
TC
|
CC
|
TC
|
CC
|
|
vegetable5qcm_scaled=0
|
1
|
1.17 (1.02-1.35)
|
0.82 (0.17-3.92)
|
1.17 (1.02-1.35)
|
0.82 (0.17-3.92)
|
|
p0
|
P= 1
|
P= 0.024
|
P= 0.81
|
P= 0.024
|
P= 6.1e-08
|
|
vegetable5qcm_scaled=1
|
0.87 (0.84-0.9)
|
1.21 (1.07-1.36)
|
1.79 (0.67-4.83)
|
1.39 (1.23-1.56)
|
2.06 (0.77-5.55)
|
|
p1
|
P= 1.9e-18
|
P= 0.0025
|
P= 0.25
|
P= 0.81
|
P= 0.15
|
|
E param by G
|
|
vegetable5qcm_scaled
|
0.87 (0.84-0.9)
|
1.03 (0.92-1.15)
|
2.18 (0.65-7.34)
|
|
|
|
p
|
P= 1.9e-18
|
P= 0.61
|
P= 0.21
|
|
|
Interaction Plot
Variable is scaled by the median sex/study specific IQR, THEN centered around median / IQR (e.g. ref = median, comparison group = median + 1IQR) 
Locuszoom

Func Annot

chr5_114126148_G_A
Allele Freq

GxE stratified by sex
sex stratified chr5_114126148_G_A_dose x vegetable5qcm_scaled
|
|
|
|
Dependent variable:
|
|
|
|
|
|
outcome
|
|
|
All (Ca=29896,Co=39838)
|
Female (Ca=14493,Co=19608)
|
Male (Ca=15403,Co=20230)
|
|
|
(1)
|
(2)
|
(3)
|
|
|
|
chr5_114126148_G_A_dose
|
1.103 (0.987, 1.219)
|
1.156 (0.987, 1.325)
|
1.060 (0.901, 1.219)
|
|
vegetable5qcm_scaled
|
0.867*** (0.836, 0.899)
|
0.873*** (0.827, 0.918)
|
0.860*** (0.815, 0.904)
|
|
age_ref_imp
|
1.000 (0.998, 1.002)
|
1.000 (0.998, 1.003)
|
1.000 (0.997, 1.002)
|
|
energytot_imp
|
1.000*** (1.000, 1.000)
|
1.000*** (1.000, 1.000)
|
1.000*** (1.000, 1.000)
|
|
sex
|
0.978 (0.942, 1.014)
|
|
|
|
chr5_114126148_G_A_dose:vegetable5qcm_scaled
|
1.197*** (1.099, 1.295)
|
1.150 (1.002, 1.298)
|
1.234** (1.104, 1.365)
|
|
Constant
|
0.976 (0.816, 1.137)
|
0.886 (0.651, 1.121)
|
1.028 (0.806, 1.251)
|
|
|
|
Observations
|
69,734
|
34,101
|
35,633
|
|
|
|
Note:
|
p<0.05; p<0.01; p<0.001
|
|
|
(PC and Study estimates omitted from table)
|
|
|
GxE term LRtest p = 2.6701e-04
|
|
|
GxE term LRtest p = 6.1220e-02
|
|
|
GxE term LRtest p = 1.3906e-03
|
GxE stratified by tumor site
cancer_site_sum2 stratified chr5_114126148_G_A_dose x vegetable5qcm_scaled
|
|
|
|
Dependent variable:
|
|
|
|
|
|
outcome
|
|
|
All (Ca=29896,Co=39838)
|
Proximal (Ca=9067,Co=39838)
|
Distal (Ca=10542,Co=39838)
|
Rectal (Ca=8432,Co=39838)
|
|
|
(1)
|
(2)
|
(3)
|
(4)
|
|
|
|
chr5_114126148_G_A_dose
|
1.103 (0.987, 1.219)
|
1.117 (0.945, 1.289)
|
1.096 (0.931, 1.261)
|
1.247* (1.076, 1.419)
|
|
vegetable5qcm_scaled
|
0.867*** (0.836, 0.899)
|
0.867*** (0.821, 0.913)
|
0.884*** (0.840, 0.928)
|
0.851*** (0.802, 0.901)
|
|
age_ref_imp
|
1.000 (0.998, 1.002)
|
0.995*** (0.992, 0.997)
|
1.018*** (1.016, 1.021)
|
0.985*** (0.983, 0.988)
|
|
energytot_imp
|
1.000*** (1.000, 1.000)
|
1.000*** (1.000, 1.000)
|
1.000*** (1.000, 1.000)
|
1.000*** (1.000, 1.000)
|
|
sex
|
0.978 (0.942, 1.014)
|
1.017 (0.965, 1.070)
|
0.785*** (0.733, 0.836)
|
1.238*** (1.183, 1.293)
|
|
chr5_114126148_G_A_dose:vegetable5qcm_scaled
|
1.197*** (1.099, 1.295)
|
1.244** (1.107, 1.381)
|
1.047 (0.903, 1.192)
|
1.170* (1.029, 1.311)
|
|
Constant
|
0.976 (0.816, 1.137)
|
0.576*** (0.353, 0.798)
|
0.100*** (-0.136, 0.337)
|
0.583*** (0.346, 0.820)
|
|
|
|
Observations
|
69,734
|
48,905
|
50,380
|
48,270
|
|
|
|
Note:
|
p<0.05; p<0.01; p<0.001
|
|
|
(PC and Study estimates omitted from table)
|
|
|
GxE term LRtest p = 2.6701e-04
|
|
|
GxE term LRtest p = 1.7517e-03
|
|
|
GxE term LRtest p = 5.3167e-01
|
|
|
GxE term LRtest p = 2.9371e-02
|
GxE stratified by study design
study_design stratified chr5_114126148_G_A_dose x vegetable5qcm_scaled
|
|
|
|
Dependent variable:
|
|
|
|
|
|
outcome
|
|
|
All (Ca=29896,Co=39838)
|
Cohort (Ca=12549,Co=24275)
|
Case-Control (Ca=17347,Co=15563)
|
|
|
(1)
|
(2)
|
(3)
|
|
|
|
chr5_114126148_G_A_dose
|
1.103 (0.987, 1.219)
|
1.009 (0.845, 1.172)
|
1.219* (1.049, 1.389)
|
|
vegetable5qcm_scaled
|
0.867*** (0.836, 0.899)
|
0.931** (0.879, 0.982)
|
0.831*** (0.791, 0.870)
|
|
age_ref_imp
|
1.000 (0.998, 1.002)
|
1.002 (0.999, 1.006)
|
0.999 (0.997, 1.001)
|
|
energytot_imp
|
1.000*** (1.000, 1.000)
|
1.000 (1.000, 1.000)
|
1.000*** (1.000, 1.000)
|
|
sex
|
0.978 (0.942, 1.014)
|
0.993 (0.936, 1.050)
|
0.965 (0.919, 1.012)
|
|
chr5_114126148_G_A_dose:vegetable5qcm_scaled
|
1.197*** (1.099, 1.295)
|
1.445** (1.209, 1.682)
|
1.118 (0.998, 1.238)
|
|
Constant
|
0.976 (0.816, 1.137)
|
3.600*** (3.146, 4.053)
|
1.100 (0.912, 1.289)
|
|
|
|
Observations
|
69,734
|
36,824
|
32,910
|
|
|
|
Note:
|
p<0.05; p<0.01; p<0.001
|
|
|
(PC and Study estimates omitted from table)
|
|
|
GxE term LRtest p = 2.6701e-04
|
|
|
GxE term LRtest p = 2.0503e-03
|
|
|
GxE term LRtest p = 6.7241e-02
|
Odds Ratios
Variable is scaled by the median sex/study specific IQR, THEN centered around median / IQR (e.g. ref = median, comparison group = median + 1IQR)
|
|
G param by E
|
|
|
GG
|
GA
|
AA
|
GA
|
AA
|
|
vegetable5qcm_scaled=0
|
1
|
1.1 (0.97-1.24)
|
1.47 (0.45-4.78)
|
1.1 (0.97-1.24)
|
1.47 (0.45-4.78)
|
|
p0
|
P= 1
|
P= 0.12
|
P= 0.52
|
P= 0.12
|
P= 2.3e-06
|
|
vegetable5qcm_scaled=1
|
0.87 (0.84-0.9)
|
1.12 (1.01-1.25)
|
2.94 (1.07-8.13)
|
1.29 (1.16-1.44)
|
3.39 (1.23-9.36)
|
|
p1
|
P= 8.4e-19
|
P= 0.038
|
P= 0.037
|
P= 0.52
|
P= 0.018
|
|
E param by G
|
|
vegetable5qcm_scaled
|
0.87 (0.84-0.9)
|
1.02 (0.93-1.13)
|
2 (0.72-5.54)
|
|
|
|
p
|
P= 8.4e-19
|
P= 0.65
|
P= 0.18
|
|
|
Interaction Plot
Variable is scaled by the median sex/study specific IQR, THEN centered around median / IQR (e.g. ref = median, comparison group = median + 1IQR) 
Locuszoom

Func Annot
